Contacts of the strand formed by residues 181 - 187 (chain B) in PDB entry 1AOX
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with GLN 181 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144B ILE 2.9 7.0 + - - +
145B ASP* 3.2 19.6 - - - +
146B VAL 2.8 25.8 + - - -
175B ILE* 5.3 2.2 - - + -
176B GLY 4.0 7.2 - - - +
177B PRO* 4.1 18.5 - - + +
180B THR* 1.3 78.3 - - - +
182B VAL* 1.3 63.8 + - - +
197B LEU* 3.4 29.3 + - + +
198B ASN* 4.1 17.2 - - - +
200B TYR 5.7 3.9 + - - +
206B MET* 5.4 0.4 - - - -
240B GLY 2.9 23.6 + - - +
242B ARG* 3.4 26.1 + - - +
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Residues in contact with VAL 182 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146B VAL* 3.2 12.8 - - + +
148B VAL* 4.5 13.9 - - + -
169B PHE* 5.2 2.7 - - + -
170B VAL* 4.7 9.9 - - + -
173B LEU* 4.1 18.2 - - + -
175B ILE* 3.9 24.0 - - + -
180B THR* 4.2 2.5 - - + -
181B GLN* 1.3 81.5 - - - +
183B GLY* 1.3 72.7 + - - +
184B LEU* 5.6 0.7 - - + -
195B PHE* 3.2 21.5 - - + -
196B ASN 3.5 11.1 - - - +
197B LEU* 3.7 7.0 + - - -
206B MET* 3.7 30.3 - - + +
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Residues in contact with GLY 183 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146B VAL 2.8 10.1 + - - +
147B VAL* 4.2 10.8 - - - -
148B VAL* 2.9 26.0 + - - +
182B VAL* 1.3 81.2 - - - +
184B LEU* 1.3 60.5 + - - +
185B ILE 4.3 0.4 - - - -
195B PHE* 3.6 12.8 - - - -
196B ASN* 4.4 0.2 - - - -
197B LEU* 3.7 17.0 - - - +
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Residues in contact with LEU 184 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148B VAL* 3.7 28.0 - - + +
150B CYS* 4.3 10.5 - - + -
166B LEU* 4.1 22.7 - - + -
182B VAL* 5.6 0.9 - - + -
183B GLY* 1.3 74.6 - - - +
185B ILE* 1.3 72.6 - - - +
186B GLN* 3.7 20.4 - - - +
193B VAL 3.8 0.2 - - - -
194B VAL* 2.8 39.8 + - + -
195B PHE* 2.9 50.5 + - + +
210B THR* 5.0 4.0 - - - +
213B THR* 4.1 11.0 - - - +
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Residues in contact with ILE 185 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147B VAL* 4.2 6.1 - - + -
148B VAL 2.9 12.1 + - - +
149B VAL* 3.4 15.4 - - + -
150B CYS* 2.8 25.3 + - - -
183B GLY 4.3 0.2 - - - -
184B LEU* 1.3 81.1 - - - +
186B GLN* 1.3 74.3 + - - +
187B TYR* 4.9 1.1 - - + -
191B PRO* 4.2 12.1 - - + -
192B ARG 3.4 15.3 - - - +
193B VAL* 4.2 17.7 - - + -
195B PHE 5.6 0.4 - - - +
226B ALA* 5.1 2.7 - - + +
229B TYR* 3.8 25.8 - - + -
230B ALA* 4.0 15.0 - - + +
234B ALA* 4.0 25.1 - - + -
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Residues in contact with GLN 186 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150B CYS* 3.0 21.5 - - + +
152B GLU* 2.9 29.6 + - - +
159B TRP* 3.4 23.6 - - + -
166B LEU* 5.2 1.1 - - - +
184B LEU* 3.7 11.8 - - + +
185B ILE* 1.3 77.6 - - - +
187B TYR* 1.3 63.9 + - - +
191B PRO* 3.6 0.3 - - - +
192B ARG* 2.7 40.1 + - - +
194B VAL* 3.6 18.9 - - + +
213B THR* 2.5 25.1 + - - +
214B SER 2.8 28.5 + - - -
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Residues in contact with TYR 187 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149B VAL* 3.7 28.9 - - + -
150B CYS 2.9 16.4 + - - -
151B ASP* 3.3 28.8 - - + +
152B GLU* 2.9 30.8 + - - +
185B ILE* 4.9 0.9 - - + -
186B GLN* 1.3 77.5 - - - +
188B ALA* 1.3 69.8 + - - +
190B ASN 3.3 14.1 - - - +
191B PRO* 3.7 10.8 - - + -
221B THR* 4.1 11.2 - - + -
222B ASN 3.7 15.5 - - - -
223B THR* 2.9 45.3 + - + +
226B ALA* 3.5 9.2 - - + -
251B VAL* 4.7 2.0 - - + +
252B VAL 4.3 1.3 - - - -
253B THR* 3.0 26.9 + - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il